Gundam Seed: An Alternative Universe
by Taisa Ayase
Summary: Gundam Seed AU: Kira is not a guy. See how Gundam Seed goes. SPECIAL NOTICE: The Chapter 1 to 3 were rewritten, while Chapters 4 & 5 were deleted
1. Trouble at Heliopolis

Disclaimer: Gundam Seed Does not belong to me

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Kira Yamato sat quietly all alone under one of the university's numerous pavilions, completing the work that her academic adviser gave her the day before while listening to the news. She giggled softly when she felt something cold lightly brush her cheek as a small green mechanical bird landed on her shoulder.

Torii is being a pest again.

She held a finger towards the little bird jumping around on her shoulder and waited for the bird to perch on her finger, still continuing to type with one hand.

"Tori?" Her mechanical pet cocked his head at her as he landed on her finger. Kira only smiled at Tori and transferred him on top of her computer's monitor as the reporter began about the ZAFT's attack on Kaoshiung, an Earth Alliance colony near them, that occurred last week.

"Kira!"

The said girl looked up, pushing away her shoulder-length hair from her eyes when a strong wind blew by, and smiled at the couple standing on the path leading to the pavilion.

"So, here you are hiding! Professor Kato was looking for you." A guy in a plain white shirt said to her, his gentle green eyes looking out from behind his wavy brown hair.

"Again?" Kira sighed , pouting slightly.

"Professor Kato said to drag you over to his laboratory once we found you." A girl in a plain orange dress smiled at her, leaning forward and regarding her with blue-green eyes full of mirth. "What is it now? Does he need your help with something again?"

"Dammit. I haven't even finished the one he gave me yesterday." Kira placed her computer on the table and leaned back against the railing surrounding the pavilion, Torii still perched on her shoulder. She stared at the news being shown on her portable computer's monitor.

"Huh? Something on the news?" Tolle approached her and looked at the news with a hand propped against the table.

"Yeah, about Kaoshiung." Kira whispered, magnifying the small media window to occupy the whole screen with a single press of a button, as Miriallia also leaned forward to watch the news.

"Ehh?" Tolle exclaimed, drawing back from her computer. "If this is from last week's information, then Kaoshiung has probably already fallen."

"Maybe." Kira whispered, turning off her computer before closing the monitor.

"Isn't Kaoshiung very close to us?" Miriallia turned to her boyfriend. "Will we be all right?"

Kira barely flinched when Torii took off from her shoulder, still staring at her computer. She raised her eyes to follow Torii's flight as Tolle reassured Miriallia that she should not worry because even though Kaoshiung is near, their country, Orb, is neutral and there is no chance that Orb would get involved in the war.

Kira smiled inwardly. She also remembered that the same thing was told to her by someone very special to her four years before.

* * *

_"You are leaving?" A then twelve- year old Kira stared at the blue- haired boy standing before her, dressed in formal travelling clothes, holding out a small green toy bird to her._

"Yes. Father and Mother wants me to come home." The boy smiled at her. "There really won't be a war between PLANT and the Earth..."

Kira quietly accepted the bird, staring at it softly, as tears swelled up at her eyes, and gently pressed the bird against her chest, as Athrun continued on.

"I don't think there's a reason to take refuge, but... Kira, you'll also be coming to PLANT sometime in the future, right?"

Kira looked up in surprise, only to smile softly at Athrun and nod her head. "Thank you, Athrun," she whispered before running up to him and pressing her lips lightly against his cheek.  


* * *

"Kira?"

Kira jerked back in surprise when Tolle's face popped right in front of her, hitting her head against one of the pavilion's wooden posts.

"What were you blushing about? Anyway, let's go." Tolle motioned her to hurry up as he and Miriallia turned around.

Kira quickly pressed a hand against her cheek and felt it hot under her touch. She always blushes whenever she remembers that one. She then stowed her computer inside her bag and ran up to Tolle and Miriallia with Torii flying after them.

Kira followed Tolle and Miriallia to the automated public transport car terminal near their university, listening to Miriallia's talk about Tolle's good grades. Then, they all stopped talking when they all heard familiar voices from in front of them.

"Huh? Miriallia?" An auburn- haired girl standing with two other girls in front of them waiting for a public transport car exclaimed when she caught sight of them.

Kira turned her eyes away as they walked up to the girl and her companions. She knew the girl, Frey Allster, the only daughter of one of the Earth Alliance's Minister. She knew Frey too well because she and Frey shared a common enmity over one guy.

"You know, Frey got a letter from Ssigh Argyle."

Kira jerked in surprise and stared at Frey. That girl managed to get one through her again but then again, Frey is Ssigh's fiancee. Then, she heard someone clear his throat from behind them. She turned her head slightly and stared at the short-haired woman dressed in formal business clothing standing behind them.

"If you aren't getting on, may we go first?" The woman smiled slightly at them, motioning towards the already waiting car.

"Oh, sorry. Please go ahead." Tolle was quick in his apology as she and Tolle stepped aside from the way.

Kira, Miriallia and Tolle watched as Frey and her friends took the next car. She almost flinched when Tolle said, "A letter from Ssigh... How surprising for Frey Allster."

Kira blushed furiously whenTolle placed his hands on her shoulders and continued, "That sounds like a formidable point. Kira Yamato."

Kira only tapped Tolle's head with a finger and said, "As if Miriallia did not do the same with you?"

With a small smile, she boarded the next car and waited for the two to board it. She thought that she managed to get Tolle to shut up with that remark, but even after they got through the security check at the Morgenroete and off the car, he would not shut up about it. It was only when they stepped into their professor's laboratory did the guy finally shut up.

"Ahh! There you are, Kira."

Kira stopped in her tracks and smiled awkwardly at the blond-haired guy working behind one of the machine, before turning to someone that caught her eye. A blond- haired boy stood leaning against one of the wall with his eyes covered by a black beret caught her eyes. It was like though she knew him. She quickly looked away and followed Tolle and Miriallia to the dark- haired guy working at the computers.

"Where's the professor?" She asked Kuzzey as he looked at her after explaining to Tolle that the stranger is a guest of their professor. Kuzzey only motioned to the door behind him.

"Kira." Ssigh called out to her, holding out a disk to her. "I have been keeping this for you. An appendix. I think."

"What?" Kira groaned softly as Ssigh approached her.

"What is it? Probably some work for Morgenroete?"

"Not interesting. Just improvements on the Frame- Set module." Kira replied, taking the disk from Ssigh. "Anyway, program analysis." She looked up hopefully at Ssigh. She did not hear Tolle creep up from behind until she felt him hold her in an headlock.

"Let's hear about the letter first." Tolle grinned at Ssigh.

"Letter?" Ssigh blinked at them.

"It's nothing." Kira quickly yelped out, stepping on Tolle's toe.

"What is it?" Ssigh persisted.

"Like I said." Tolle said, only to be silenced when Kira stepped on his foot again.

"It's nothing." Kira shouted.

"What is it, Tolle?" Ssigh insisted once again. "Just tell me!"

"Stop it." Miriallia butted in.

"Let go! You're choking me." Kira stepped on Tolle's feet again.

"It won't go that way."

Minutes later working while waiting for their professor, they heard something loud before the laboratory shook and equipment fell down. Kira braced herself with the help of the computer monitors as she heard Ssigh whisper ,"Meteorites?", from beside her. But she immediately felt it was not.


	2. We Meet Again

Disclaimer: Gundam Seed Does Not Belong to Me.

* * *

Kira flinched slightly when a small piece of debris hit her shoulder. She has been following their professor's guest who just suddenly ran out of the shelter. She had to leave Ssigh and the others to keep the guest free from harm. 

"What in the hell do you think you are doing?" She shouted as soon as she caught up with the unnamed guest and grabbed hold of his shoulder, turning him around sharply. "They told us to go to the shelter!"

"Why did you follow me?" The guy shouted back. "You should hurry up and leave."

Kira barely had the time to reply when a large explosion occurred from behind her. She instinctively grabbed hold of the guy by the wrist, protecting his body with her own, when the shockwave passed through them. She nearly jerked back in surprise when she opened her eyes and stared at the guy.

"A... girl?" She gasped out in surprise, blinking innocently.

"As if you're not. What did you think I was until now?" An orange- eyed blond girl glared at her angrily.

"No... It is just." Kira quickly let go of the girl's wrist. Then, she looked behind her as a second blast occurred near them.

"Forget it! Just go!" The girl shouted at her, turning back towards the undamaged part of the hallway. "I have something I must confirm."

"Go where?" Kira exclaimed angrily. "I can't go back anymore." She drew back in surprise when the girl turned back at her and regarded her with serious eyes. Kira let out a soft sigh before grabbing hold of the girl's wrist and saying, "This way", and pulled the girl to another corridor.

"Let go, you idiot." The girl shouted at her back as they ran through the hallway, the entire structure shaking with every explosion. "If it comes to this, I..."

"It's all right." Kira whispered, glancing at the girl and seeing her frightened face. "We will be saved. If we go to the factory, there should still be a shelter."

They both came to a complete halt as soon as they came out of the corridor, only to be welcomed by guns firing and two unbelievable objects. Kira stared in surprise as she realized that the two objects were Mobile Suits. Startled, she turned to the girl beside her when the latter fell to her knees, muttering, "I knew. The Earth army's new mobile weapon... Father, you traitor!" the girl shouted, tears gathering at her eyes.

Kira drew back from the railing when she saw with the corner of her eye, one of the armed factory workers points his weapon at them. Then, she grabbed the girl's wrist and pulled her to her feet. She pulled the girl to safety as bullets were fired at the place where they were only seconds ago. She pulled the girl towards a nearby shelter, ordering the latter to pull herself together and keep on running.

"See? There are people taking shelter here." She glanced momentarily at the girl following her as they came to a halt in front of the only remaining shelter, pressing the call button.

"There is still someone out there?" The intercom quickly replied.

"Yes, a friend and I! Please open the door." Kira quickly spoke up.

"Two?"

"Yes!"

"We are already full. Shelter 37 in the left block is still available. Can you get there?"

Kira leaned back to study their smoke- covered surroundings in a heartbeat, before pressing the communications button again. "Then at least take one of us." She shouted. "A younger girl. A guest!"

"We understand. I'm really sorry."

Kira quickly pushed the girl inside the elevator leading down to the shelter as soon as the door opened. She barely gave the girl time to struggle back when she sealed the door. She stepped away from door and immediately ran towards the left block in spite of the explosions at the factory floor below her. Then, she caught sight of a green- uniformed ZAFT soldier aiming a factory worker from behind. She skidded to a halt and quickly called out a warning. She grimaced slightly as the soldier was shot before she was called out by one of the factory workers, a woman by the sound of her voice.

"I'll head for the shelter in the left block. Don't worry about me." Kira quickly shouted back in reply.

"The only thing left is that door."

Kira yelped in surprise when the steel door was blown in, sending her reeling to the ground. She quickly picked herself up and stared at the remains of what used to be one of the most secure airlocks in the colony. She began running towards the direction of the female factory worker when the latter called out to her. Jumping effortlessly over the railing, she landed on one of the Mobile Suits lying around and gasped in surprise when the factory worker who called out to her was shot in her arm. Without thinking of the danger, she quickly ran up to the woman and caught her as she fell. She looked up when she saw with the corner of her eye a red-space suited ZAFT soldier run up to them with a dagger in hand. A startled gasp escaped her lips when she caught sight of the soldier's face through the faceplate.

"Athrun?" She gasped out.

The soldier stopped in midstrike, and stared at her, whispering, "Kira?"

Kira stood up from her knelt position and stared at Athrun in shock. She never expected to see him this way again. It was all broken when Athrun quickly jumped back as the factory worker pointed a gun at his direction. Kira made a move to follow Athrun, only to be pushed inside the cockpit of the Mobile Suit.

"Go behind the seat." The factory worker ordered her as soon as the latter entered the cockpit and closed the hatch. Kira quickly did what the woman ordered her, and listened to the woman mumble to herself that she can at least move the machine. Kira stared at the side monitor across her as the monitors came alive and stared at the Mobile Suit beside theirs. She could not believe that she just saw her childhood friend. Then, she turned towards the operations panel, just as words flashed on the screen.

"Gundam?" She whispered, reading the panel. Kira quietly watched as the woman operated the Mobile Suit, keeping a firm grip on the pilot seat for balance. The Mobile Suit had almost lost its balance when its surroundings exploded. She let the woman pilot the Mobile Suit out of the factory, barely keeping her balance as the Mobile Suit struggled to keep standing. She gasped in surprise when small magnified screens popped up all over the monitors, and she saw her friends running away from them. She held on even more as the Mobile Suit staggered back after being hit by one of ZAFT's Mobile Suits. She finally lost her balance when the woman, after ducking away from the enemy Mobile Suit's attack, caused the Mobile Suit to land hard. She fell hard on the woman's lap.

"Stay in the back! Do you want to die?"

Kira quickly apologized at the woman, only to catch sight of the enemy Mobile Suit lunged towards them with a sword in hand.


	3. Athrun and Kira

Disclaimer: Gundam Seed Does not belong to me

* * *

"We're the only ones who can protect the Archangel. If we can't do it, everyone will die," Kira whispered to herself, her eyes lowered, as Chief Murdock tugged on her seat straps making sure that they were tight before rapping the top of her helmet. Kira jerked her head back, holding her helmet.

"You all right, kid? You look a bit distracted. We're getting ready to launch to Strike."

She's scared. Kira gripped the controls tightly as she stared at the chief mechanic with bewildered eyes, her heart thumping loudly against her tight chest. She was so afraid.

"Kid?"

"Mr. Murdock, can I ask a favor?" her voice came out in a soft whisper. Murdock had to duck back into the cockpit just to hear her. "Torii- my robot. Can I bring it along?"

"Robot bird?"

"Yes. I placed him in the locker room. You can deactivate him. The power switch is under his right wing. I-," Kira paused and bit her lip, "I kind of need him. Can someone get him for me?"

"Sure, kid." Murdock grinned at her before ducking out of the cockpit to shout at one of the younger mechanics to get it. "Don't worry, kid," he patted her head. "Just keep that Laurasia-class ship busy and protect the Archangel."

"I know," Kira nodded as a mechanic handed the robot bird to Murdock. With Torii safely clipped at her side, Kira closed the hatch, catching the encouraging smile that Murdock threw at her before he disappeared out of sight, and took a deep breath, waiting for the OS to finish booting up.

"Kira!"

The said girl jerked forward and stared at the brown-haired girl smiling back at her from a small screen on top of her monitor as a loud hissing sound she identified as that of the linear catapult's locks engaging reached her ears. "Miriallia? What are you-?

"I'm taking care of the battle control for the Mobile Suit and Mobile Armor from now. Pleased to meet you," Miriallia winked at her, dissolving some of her nervousness with the casual gesture.

"It's good to be of service," an off-screen soldier scolded her friend as she felt the tell-tale shudders of Strike being armed.

"Kira, what you're going to use is called the Aile Striker pack."

"Got it," she nodded, lowering the visor of her helmet. "Kira Yamato, Strike Gundam launching," she announced.

The sheer force of the catapult launch had pressed her against the seat. Gritting her teeth, she quickly pulled Strike to a straight flight, switching on the Phase-Shift Armor as she did. Her proximity alarm immediately went off as her radar picked up a rapidly-approaching object coming from the direction of the Laurasia-class warship blocking Archangel's way. Ignoring the loud alarms, she gripped the controls harder, calming her racing pulse.

"One unit," she whispered, her eyes darting toward the monitor showing Archangel. "Just protect, he said. That lieutenant-"

She was pulled out of her musings when her camera panned in on the incoming object from the Laurasia warship, a small gasp escaping her lips when she recognized the object.

"That Mobile Suit... Athrun!" She cried out, putting away Strike's rifle, and pulled out its beam saber. She didn't want to fight him. Her heart skipped a beat when Aegis passed by her, eyes wide with shock.

"**Kira!**"

"Athrun?" Her eyes were drawn to the small screen showing her childhood friend.

"**Stop this already! Put your saber away, Kira! We're not enemies, right? Why do we have to fight?**"

He thought they were enemies? She was just as confused as he is. She didn't know why they needed to fight one another.

Kira lowered her eyes for a second before turning back to the Aegis pilot. "Athrun-"

"**You're also a Coordinator!**" Athrun shouted at her as Strike and Aegis circled one another, oblivious to the ongoing battle between Archangel and the other three stolen EA Mobile Suits. "**Why do you have to fight against us?**"

Kira flinched. Did he really think she's fighting them because they're Coordinators? Why did he have to think it that way?

Sounds of explosions behind her brought her out of her musings, and she glanced at the monitor showing Archangel, her eyes widening at what she saw. "Archangel is-", she gasped loudly, quickly turning Strike about, only to jerk back on her controls when Aegis suddenly appeared in front of her.

"**Stop it, Kira!**"

"**Athrun!**" She stared at her childhood friend's face, her chest constricting painfully at his angry expression.

"**Why are you in the Earth Alliance? Why do you ally yourself with the Naturals?**"

"**I'm not with the Earth Alliance!**" Kira shouted, pullingStrike away from Aegis. She needed to go back to Archangel. She had to go back. She has to protect everyone.

Athrun was surprised by Kira's loud declaration, following her mobile suit around.

"But my friends- **my friends are on board that ship!**"

"Kira-", the Aegis pilot whispered, staring at Kira's face.

"**You too! Why ZAFT? Why are you in the war?**" Kira shouted as she tried to return to Archangel, only to find Aegis blocking her way the entire time. " **'I hate war,' you said that, didn't you? Why did you attack Heliopolis?**"

"Because Naturals who don't understand the situation built this thing."

"**Heliopolis is neutral! Even I, but-**"

She was cut off when her proximity alarm went off again, dodging several rifle shots from another mobile suit. "X102, Duel?" She panted softly, her heart hammering painfully in her chest. "Then, that also-" She raised her shield just in time to block another shot.

It took her everything to keep on dodging Duel's shots, her seat straps digging painfully into her shoulders at every sudden turn she made. She simply didn't have anything left to use to attempt to return to Archangel. Where is Lieutenant La Fllaga? She's getting worried. Things are getting difficult minute by minute, and she might even get hit if things continue as such.

Putting her beam saber away, Kira brought out Strike's beam rifle, a targeting monitor sliding in front of her. To survive, she's going to need to fight back. Aiming for Duel, she fired shot after shot at the Mobile Suit. She just needed to distract them a little more.

She flinched when Duel dodged her last shot with ease taking out its beam saber. She quickly blocked his sword strike with her shield, pulling back Strike from Duel's strike range. She continued firing at Duel keeping her distance from the said mobile suit. She couldn't afford to get into a close combat fight with a more experienced pilot.

"**What the-!**" She shouted, ducking from a series of gunfire. Her fear returned when she found herself surrounded by four mobile suits, Duel and Aegis included, fear constricting her chest. She spent every last power she had dodging and evading the three mobile suits attacking, somewhat thankful that Athrun hadn't move at all.

A message from Archangel caught her attention and a small smile of relief lit up her face as she dodged another attack. Lieutenant La Fllaga was successful, and her gut feeling tells her that her opponents just got the news. She had just turned Strike around when Archangel fired a retreat signal.

But Duel's pilot wasn't just about let her go so easily. Kira dodged another of his attacks, firing back as she pulled Strike into reverse, gritting her teeth when the two other mobile suits rejoined Duel in its attacks.

"**Damn it! At this rate-!**" Kira didn't have time to finish her rant as a loud alarm blared behind her head. She quickly turned Strike around and took a shot at the fast-approaching Duel, only to feel her throat constrict painfully in fear. There was nothing coming out of the barrel.

"**Power's out**," she cried out just as the low power alarm went off. "**Then, the armor-**"

_She was afraid. She had to get out. She didn't want to die. She didn't want to die just yet._

Tears were running down her cheeks as Duel chased after her. She tried flying off, but he was too close. She's not going to make it.

It was just pure instinct. She had let go of the controls, curling up into a ball, covering her head with her arms, sobbing loudly. Strike dipped slightly in its flight but she didn't care. She was afraid.

A bone jarring jolt, then a loud shout over her radio.

"**Kira!**"

_She was going to die._ Her chest constricted painfully.

"**Kira! Can you hear me?**"

_She's going to die. _She couldn't breath.

"**Kira!**"

_She didn't want to die._ She couldn't move.

"**Kira!**"

"**I don'twant to die!**"

Athrun was stunned by the panic-stricken scream that came over his radio. "**Kira!**"

"**I'm afraid! I'm afraid! I'm afraid! Otousan! Okaasan! I don't want to die! I'm afraid!**"

"**Kira! Answer me!**" Athrun felt a lump grow at his throat at the sight of Kira's curled form on his monitor as he continued to ignore Yzak's shouted demands. "**Kira!**"

"**I'm afraid. I don't want to die, Athrun!**"

"**I'm not going to let you die, Kira!**" Athrun shouted, gripping his controls harder. "**So stop crying. I'm not going to let you die.**"

"I'm afraid. I'm afraid. I'm afraid," Kira continued to chant in between her sobs.

"**Kiddo!**"

Athrun swore loudly as his proximity alarm went off and a strong shudder ran through Aegis' entire frame. It was the Mobile Armor from before.

"**I don't want to die!**"

"**Then get yourself together, kid! Do you want your friends to die? There's still another big ship behind us**," shouted Mwu La Fllaga, continuing his attack on Aegis. "**Archangel's launching the Launcher Pack! Retreat and get to it!**"

She didn't stop crying even when she uncurled herself from her seat, grasping the controls with shaking hands, tears floating around her helmet. She cried even harder when she felt her stomach drop when Aegis let Strike go to attack the Lieutenant's Moebius Zero. She flew toward Archangel ignoring the shots flying past her. She was still crying when she disengaged the Aile Pack in preparation for receiving the Launcher Pack, her sobs increasing in intensity when an alarm went off.

"**Kira!**"

Athrun's loud scream over the radio was the last thing she heard before she was slammed forward against her straps, sparks flying all over the place and darkness enveloped her consciousness.

* * *

Ohhhhh, cliffie... 

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